Conductive media for electrophoresis

ABSTRACT

A series of low molarity conductive media based on non-buffering univalent cations, such as sodium chloride-sodium acetate (SCA), sodium boric acid (SB), lithium boric acid, and lithium acetate mitigate the “runaway” positive feedback heating loop produced by conventional media containing biological amine buffers and permit improved DNA electrophoresis under the conditions of low salt concentration. These media serve well in ultra-fast DNA electrophoresis and in high-resolution separations of RNA and DNA fragments.

This invention was funded using U.S. government finds under NIH awardCA62924. The U.S. government therefore retains certain rights in theinvention.

FIELD OF THE INVENTION

The invention relates to the field of electrophoresis. In particular itrelates to electrophoresis of biological macromolecules.

BACKGROUND OF THE INVENTION

It has been nearly three decades since the invention of DNAelectrophoresis (1-5), and molecular biology laboratories still relyupon the separation of DNA, from plasmid DNA to PCR products, by use ofdenaturing or non-denaturing gel electrophoresis (1). Current conductivemedia for DNA electrophoresis are largely restricted to legacyTris-acetic acid-disodium EDTA (TAE) and Tris-boric acid-disodium EDTA(TBE) at substantial ionic strengths, leading to higher cost andexcessive heat generation and limiting the voltage and speed ofelectrophoretic runs (for description of buffers see Table 1).Investigators have compared and analyzed TAE and TBE buffers in DNAelectrophoresis; however, to our knowledge no one has substantiallyinvestigated the simplification and substitution of components of thesebuffers to achieve a more efficient conductive medium for DNAelectrophoresis (6). Conductive media for DNA electrophoresis derivedessentially unchanged from RNA gel methodology, which in turn wasadapted from a subset of buffers used for protein electrophoresis in theearly 1960's (4, 7). The most common DNA electrophoretic media havecontained Tris, an organic amine, as their primary cation; the firstedition of Molecular Cloning (1982) contained a table of the threecommonly used buffers for agarose gel electrophoresis: Tris-aceticacid-disodium EDTA, Tris-phosphate-disodium EDTA, and Tris-boricacid-disodium EDTA (1, 8). Presently, Tris-based buffers (TBBs) remainpredominant in nearly all molecular biologic research and clinicallaboratories (9). TBBs usually contain between 40 to 80 mM Tris(predominantly ionized), corresponding anion concentrations, as well astrace amounts of different forms of EDTA (1-2 mM), which could inhibitnucleases and certain enzymatic reactions. These high concentrationswere historically supported by a preference to avoid ions of highmobility (7), to overcome detrimental effects on resolution ofDNA-borate complexation by use of higher borate concentrations (6, 10),and to avoid the problems of dilute TAE media (10, 11). Tris is at timesused with or replaced by other organic amines that buffer pH in thebiological range.

It is well established that heat generation is a primary source ofproblems in gel electrophoresis, is responsible for sample diffusion,convection, denaturation, and poor gel integrity, and limits the abilityto run gels at a high voltage (12). Ohm's law and the power lawinterrelate voltage (V), current (I), and power (P)(13, 14). Powerconsumed in the electrophoresis system manifests as heat; heatgeneration=P=VI. These interrelated variables are affected by ionicconductance due to choice of salts and ionized components in proportionto their particular concentrations in the media used in electrophoresis.The concentration of salts also determines the stability of thedouble-helical structure of DNA—a melted, single-stranded DNA (ssDNA)structure being desirable for certain DNA electrophoretic techniques.

There is a need in the art for improved conductive media for carryingout electrophoresis of nucleic acids.

BRIEF SUMMARY OF THE INVENTION

In a first embodiment of the invention a method is provided forelectrophoretically separating polynucleotides of different sizes. Aconductive medium is used to carry a current from one electrode toanother. The conductive medium comprises at least 0.5 mM anions inaddition to any chloride anions which are optionally present. Theconductive medium comprises less than 50 mM of total ions and does notcontain an organic amine biological buffer. Alternatively, theconductive medium comprises one to 30 mM of total ions, inclusive, andcontains an organic amine biological buffer at a concentration of lessthan 10 mM. Polynucleotides are spatially separated between theelectrodes.

In a second embodiment of the invention a gel is provided for separatingpolynucleotides according to length of the molecules. The gel comprisesa matrix substance and a conductive medium. The conductive mediumcomprises at least 0.5 mM anions in addition to any chloride anionswhich are optionally present The conductive medium comprises less than50 mM of total ions and does not contain an organic amine biologicalbuffer. Alternatively, the conductive medium comprises one to 30 mM oftotal ions, inclusive, and contains an organic amine biological bufferat a concentration of less than 10 mM. Polynucleotides are spatiallyseparated between the electrodes.

In a third embodiment of the invention a solution is provided for makinga gel for separating polynucleotides according to length of themolecules. The solution comprises: a conductive medium and apolymerizing agent for polymerizing a gel matrix substance. Theconductive medium comprises at least 0.5 mM anions in addition to anychloride anions which are optionally present. The conductive mediumcomprises less than 50 mM of total ions and does not contain an organicamine biological buffer. Alternatively, the conductive medium comprisesone to 30 mM of total ions, inclusive, and contains an organic aminebiological buffer at a concentration of less than 10 mM. Polynucleotidesare spatially separated between the electrodes.

In a fourth embodiment of the invention an electrophoretic apparatus isprovided. The apparatus comprises a gel, two or more reservoirscontiguous with the gel, and an anode and a cathode in contact with thereservoirs. The reservoirs and the gel comprise a conductive mediumwhich comprises at least 0.5 mM anions in addition to any chlorideanions which are optionally present, and less than 50 mM of total ions,wherein the conductive medium does not contain an organic aminebiological buffer. Alternatively, the conductive medium comprises one to30 mM of total ions, inclusive, and contains an organic amine biologicalbuffer at a concentration of less than 10 mM.

In a fifth embodiment of the invention a method is provided for forminga gel. A gel matrix substance and a conductive medium are mixed to forma pre-gel mixture. The conductive medium comprises at least 0.5 mManions in addition to any chloride anions which are optionally present,and less than 50 mM of total ions; the conductive medium does notcontain an organic amine biological buffer. Alternatively, theconductive medium comprises one to 30 mM of total ions, inclusive, andcontains an organic amine biological buffer at a concentration of lessthan 10 mM. The pre-gel mixture is incubated under conditions in which agel forms.

In a sixth embodiment of the invention an electrophoretic apparatus isprovided. The apparatus comprises a viscous liquid in a container, andan anode and a cathode in contact with the viscous liquid. The viscousliquid comprises a conductive medium which comprises at least 0.5 mManions in addition to any chloride anions which are optionally present.In addition, the conductive medium comprises less than 50 mM of totalions and does not contain an organic amine biological buffer.Alternatively, the conductive medium comprises one to 30 mM of totalions, inclusive, and contains an organic amine biological buffer at aconcentration of less than 10 mM.

In a seventh embodiment of the invention a kit for forming a gel isprovided. The kit comprises a solid mixture for dissolving in water toform a conductive medium, a gel matrix substance, and instructions. Theconductive medium comprises at least 0.5 mM anions in addition to anychloride anions which are optionally present, and less than 50 mM oftotal ions. The conductive medium does not contain an organic aminebiological buffer. Alternatively, the conductive medium comprises one to30 mM of total ions, inclusive, and contains an organic amine biologicalbuffer at a concentration of less than 10 mM. The instructions describehow to form a gel by dissolving the solid mixture in sufficient water toform the conductive medium.

In an eighth embodiment of the invention a kit is provided for forming agel. The kit comprises a concentrated liquid for diluting in water toform a conductive medium, a gel matrix substance, and instructions. Theconductive medium comprises at least 0.5 mM anions in addition to anychloride anions which are optionally present, and less than 50 mM oftotal ions. The conductive medium does not contain an organic aminebiological buffer. Alternatively, the conductive medium comprises one to30 mM of total ions, inclusive, and contains an organic amine biologicalbuffer at a concentration of less than 10 mM. The instructions describehow to form a gel by diluting the concentrated liquid in sufficientwater to form the conductive medium.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1F show analysis of the effects of conductive media on currentand temperature during electrophoresis. (FIG. 1A) Heat generation byconductive media over time during electrophoresis at constant voltage(150V). (FIG. 1B) Conductance of media over time at constant voltage(150V). (FIG. 1C) The effect of external heating of conductive media onconductance. Solutions were heated or cooled to 17° C., 24° C., and 30°C. and the current immediately measured. (FIG. 1D) The effect of traceNaCl and NaAc, in conventional media Salts were spiked into a simplifiedTris-based solution at 150V and current immediately measured. (FIG. 1E)The effect of Tris on conductance. Tris was spiked into SB, at amountsup that of conventional media, at 150V and current immediately measured.(FIG. 1F) The concentrations of different forms of EDTA used inelectrophoretic media were compared at constant voltage (150V) duringelectrophoresis. Lines connect the measured data points (filledcircles).

FIG. 2 shows a schematic representation of the “runaway” positivefeedback loop created by an increase in temperature and conductance ofthe conductive media during electrophoresis.

FIGS. 3A-3C show SCA (sodium chloride and acetate) islands. (FIG. 3A)The graph plots the empirical nature of the performance of SCA mediaFIG. 3B) LoSCA (10 mM NaAc and 2.5 mM NaCl) run at standardelectrophoretic conditions (8 V/cm, >1 hr). (C) HiSCA (11 mM NaCl and1.5 mM NaAc) run at standard electrophoretic conditions (8V/cm, >1 hr).Ladder and an unpurified PCR product in reaction buffer were appliedusing the indicated loading solutions (see Materials and Methods).

FIGS. 4A-4C show SB (sodium boric acid medium) performance in agaroseDNA electrophoresis. (FIG. 4A) An SB gel run at standard conditions(8V/cm). A ladder and unpurified PCR product in reaction buffer wereapplied using different loading solutions, as indicated. SB gels hadflexibility in loading conditions. (FIG. 4B) An SB gel run fast (30V/cm,13 min). All lanes used SB-based loading solution. The ladder is run asthree replicates. (FIG. 4C) Gel-extracted restriction digested plasmidDNA from an SB gel is analyzed on an SB gel. Two separate DNA insertswere run.

FIGS. 5A-5C show electrolyte exhaustion and pH changes over time. (FIG.5A) Electrolyte exhaustion. Conductive media were tested for exhaustionby plotting the current at constant voltage (200V). (FIG. 5B) pH changesof conductive media analyzed in the cathodic electrode duringelectrophoresis (10V/cm, 1 hr). (FIG. 5C) pH changes of conductive mediaanalyzed in the anodic electrode during electrophoresis (10V/cm, 1 hr).

FIG. 6A-6C. Conductive media at one-mM cation concentration rapidlyseparate low molecular weight DNA in agarose. All cations were pairedwith boric acid. Cations are represented by their elemental symbol,except for ethanolamine (Ea). ΔT is given in ° C. and current inmilliamperes. (FIG. 6A) 100 bp resolution. 250V were applied for 25 min.A DNA marker (Invitrogen) had fragments at 100, 200, 300, 400, 500, and650 bp. (FIG. 6B) 20 bp resolution. A very high voltage (1000 V) wasapplied for 5.5 minutes (as compared to the conventional 90 min). A DNAmarker (GenSura) had fragments at 20, 40, 60, 80, and 100 bp. The pH ofthe conductive media at 1 mM was approximately 8.2. (FIG. 6C) 1 bpresolution. ssDNA oligomers were run on 3% agarose gels at 29V/cm for 25min, with an initial gel temperature of 37° C. The samples weredenatured by heat (70° C. for five min.) prior to loading on the gel.Each lane was loaded with a different size oligomer mixed with a35-oligomer.

FIG. 7A to 7B. Fast separation of high molecular weight DNA and RNAusing low-molarity conductive media (FIG. 7A) 1000 bp resolution. A highvoltage (300V) was applied for less than 30 min. The illustrated DNAmarker (Invitrogen) comprises 1.6 kb, and 2 Kb to 12 Kb in 1 Kbincrements. The pH of 5 mM lithium acetate was approximately 6.5. (FIG.7B) Low-molarity media used to separate RNA. 1.0% agarose-formaldehydegels were run at 40V/cm for 10 minutes. An RNA marker (New EnglandBiolabs) had fragment sizes of 461 to 4,061 bases as indicated. Lane 1represents a 5 mM lithium acetate agarose gel and lane 2 represents a 5mM sodium boric acid gel (pH=6). The initial current for the sodiumboric acid medium was 44 mA and the final current was 47 mA. The ΔT was8° C. The initial current for the lithium acetate medium was 56 mA andthe final current was 80 mA. The ΔT was 9° C. In contrast, a 1×MOPS (20mM MOPS, 7 mM sodium, 1 mM EDTA)(not shown) at the same voltage had aninitial current of 93 mA and a final current of 119 mA. The ΔT was 15°C.

DETAILED DESCRIPTION OF THE INVENTION

It is a discovery of the present inventors that high-resolutionelectrophoretic separation of biological macromolecules, such aspolynucleotides, can be advantageously accomplished using low-saltconditions. Moreover, pH buffering capacity is not of criticalimportance. Such conditions lead to lower heat generation, allowingrapid electrophoresis at higher voltage than possible at higher ionicstrength, and permit the separation of short DNA fragments and ssDNA athigh resolution under more convenient conditions. For example, very lowionic conditions for the electrophoresis of ssDNA in a gel enableelectrophoresis to readily occur while reducing or eliminating the needfor chemical additives to the gel, such as urea and formamide, thatserve to ‘melt’ or maintain DNA in a melted (single-stranded)conformation (FIG. 6C).

Electrophoresis is the process by which electrically charged biologicalpolymers can be moved through a solvent in an electric field. Thesolvent can be a liquid or a gel. To prevent diffusion, it may bedesirable for the liquid to have a high viscosity. A gel or viscousmedium for conducting electrophoretic separations of nucleic acids canbe made by any matrix substance known in the art. These includepolyacrylamide, agarose, starch, and combinations of such matrixsubstances. The matrix substance may be cross-linked to increasemechanical strength. The matrix substance may have a chromatographiceffect by adsorbing or sieving, but such is not necessary.

Buffers may be used in the practice of the invention, but they are notrequired. Organic amine biological buffers, such as HEPES, Tris, TAPS,bicine, ACES, MES, CAPSO, and MOPS are commonly used in biologicalapplications. These buffers are used for buffering solutions in thephysiological range of 6.0 to 8.5. Such buffers are not required in thepractice of the invention. If used, the organic amine biological bufferare present at a concentration of less than 10 mM, less than 5 mM, lessthan 2.5 mM, or less than 1 mM.

The conductive media of the present invention can be used in anyelectrophoretic configuration known in the art. The electrophoresis canbe carried out in liquid, semi-solid, or gel, for example. The shape ofthe gel can be a slab, a thin layer, a column, a capillary, etc. Viscoussolutions and gels form a continuum physically and in scientificparlance; indeed, viscous solutions of polymers capable of a sievingproperty, such as are solutions formed by linear polyacrylamide, areoften referred to as “gels.”

Kits for forming gels typically are packaged in a container, which isdivided or undivided, and which may contain additional containerswithin. The components for forming the conductive medium may be suppliedin separate containers or pre-mixed. The components may be in a liquidor solid form. If the components are in a liquid form, the kit willtypically contain instructions for diluting the liquid. If thecomponents are in a solid form, the kit will typically containinstructions for dissolving the components. The instructions may beverbal or pictorial. They may be printed on paper or embodied on anelectronic medium, such as a compact disk. The instructions may beembodied in the kit as a website address. The kit may optionallycomprise other items, such as a gel matrix substance, e.g. agarose orpolyacrylamide, cross-linking agents, polymerizing agents, containers inwhich to form a gel, molecular weight standards, and dyes.

While some ions are necessary for electrophoresis to occur, theinventors have found that a high concentration of ions is not necessary.At a minimum, the conductive medium of the invention should have atleast 0.5 mM of anions which are not chloride ions. Chloride ions,however, need not be present. The concentration of anions may be atleast 0.5 mM, at least 5 mM, at least 10 mM, at least 15 mM, or at least20 mM. For particular circumstances, the concentration of total ions isdesirably less than 40 mM, less than 30 mM, less than 25 mM, less than20 mM, less than 15 mM, less than 10 mM, or less than 5 mM. The pH ofthe conductive medium is preferably greater than 5, greater than 6, orgreater than 7, but less than 11, less than 10, or less than 9.

Any cations and anions can be used within the concentration and pHparameters set forth above. Anions which can be used advantageouslyaccording to the invention include chloride, carbonate, acetate, borate,phosphate, formate, and salicylate. Cations which can be used includewithout limitation sodium, potassium, ethanolamine, ammonium, lithium,rubidium, and cesium. Mixtures of cations and mixtures of anions can beused. Thus the concentration of any individual ion may fall below astated lower limit, so long as the total concentration falls within thestated ranges.

A capillary enclosure in its most common form is a capillary tube, lessthan 2 mm in internal diameter, made of fused silica that guides asingle electrophoretic path of the polynucleotides being separated,appropriate for loading a single sample in a limited time period. Anessentially equivalent capillary enclosure that guides a single path ofelectrophoretic separation can be made of other materials or drilledinto a solid material, such as employed in microfabricated devices. Acapillary enclosure is generally distinguished from the other majorelectrophoretic design, that of slab gel electrophoresis, by anindividual capillary unit having a small cross-sectional area (i.e.,less than about 5 mm) and by its containment of only one electrophoreticpath, whereas individual slab gels usually comprise many paths inparallel, permitting loading of multiple samples and simultaneouslyseparating them spatially within the same gel.

While the invention has been described with respect to specific examplesincluding presently preferred modes of carrying out the invention, thoseskilled in the art will appreciate that there are numerous variationsand permutations of the above described systems and techniques that fallwithin the spirit and scope of the invention as set forth in theappended claims.

EXAMPLES Example 1—Materials and Methods

Studies of conductance, temperature, and voltage used a horizontal gelrig (MGU-500, CBS, Del Mar, Calif.) and a power source that providedcurrent readings at set voltages (FB 570, Fisher Biotech, Pittsburgh,Pa.). All media were analyzed at the same volume (650 ml) in thereservoir. 1.2% agarose (Type I: low EEO Agarose, Sigma, St. Louis, Mo.)gels containing 0.2 microgram/ml ethidium bromide (EtBr) (FischerScientific, Fair Lawn, N.J.) were used except as noted. Tris-EDTA (TE)solution was purchased from Invitrogen, Carlsbad, Calif. (1×TE: 10 mMTris-HCl, 1 mM EDTA).

A DNA marker (1 Kb plus, Invitrogen) was used as a test sample. Sodiumchloride (NaCl), sodium hydroxide (NaOH), sodium acetate (NaAc),potassium hydroxide (KOH), and potassium chloride (KCl) were bought fromJ. T. Baker (Phillipsburg, N.J.). Tris and all forms of EDTA were boughtfrom USB (Cleveland, Ohio). A 1× loading solution matched to eachconductive media was used as indicated in the figures. All loadingsolutions contained 0.5% N-lauroyl sarcosine sodium salt (ICNBiochemicals, Cleveland, Ohio), 0.05% orange G (Sigma), and 20% glycerol(USB) in a given conductive medium. Gel extraction was performed withthe Qiagen Gel Extraction Kit (Qiagen, Valencia, Calif.). Otherchemicals were bought from Sigma Gel resolution studies were performedin MGU-500 and MGU-502T units (CBS). Gel resolution studies werevalidated and polyacrylamide gels were used in larger vertical gel rigs(SE 600, Hoefer Scientific Instruments, San Francisco, Calif.).

For denaturing gels, a 24:1 polyacrylamide (Grade A Accurate Chemicaland Scientific Co., Westbury, N.Y.) and bis-acrylamide (USB) solutionwas used to make a final concentration of 20% acrylamide (0.2% EtBr), 6M urea in the Hoefer rig using a 1 mm spacer. Ammonium persulfate (J. T.Baker) and TEMED (USB) were used to polymerize. Two oligos (21 and25-mers) of complimentary sequence were analyzed denatured and annealed(Integrated DNA Technologies, Coralville, Iowa).

Example 2—Conventional Media and Heat

A thorough analysis of the critical properties of widely used bufferedmedia for DNA electrophoresis was performed. At constant voltage, wefound that a positive feedback loop existed between the temperature ofthe buffer and the current for all TBBs (FIG. 1 a-c). At constantvoltage, TAE and TBE experienced increased temperature and current overtime (FIG. 1 a,b). To verify that temperature and current were directlyinterrelated (a known feature of electrolyte solutions) we manipulatedthe temperature of the buffered media (13, 14). For all TBBs, externalheating of the conductive media resulted in a direct increase in current(FIG. 1 c). Superfluous sodium ions as well as the high amount of Trisions (Table 1) in these buffers were found to be responsible forproducing unnecessary current and limited the ability to run gels at ahigh voltage; the addition of millimolar amounts of NaCl or NaAc to asimple Tris-acetic acid (30 mM Tris) medium increased current almosttwo-fold under constant voltage (FIG. 1 d). Since a reduced currentwould directly mitigate heat generation, the results supported thenotion that low ionic strength buffers would be optimal for DNAelectrophoresis and that superfluous ions should be avoided.

We explored the constituents of TBE and TAE as prepared by majorbiotechnology suppliers, laboratories within our institution, andstandard laboratory manuals (such as Molecular Cloning) (1, 9). Variousprotocols use either free acid EDTA (Invitrogen), disodium EDTA(Molecular Cloning)(1, 9), or tetrasodium EDTA (USB) (see Table 1).Although this might appear to be a trivial difference, media containingequimolar EDTA of different forms behaved quite differently. As expectedfrom the above results (FIG. 1 d), media containing EDTA (acid) had theleast initial current and maintained a reduced current over time ascompared to the two other forms of EDTA that contained additional sodium(FIG. 1 e). We concluded that amounts of sodium capable of generatingsignificant current are included in common media. Another protocolspecified NaAc to be added to TAE along with disodium EDTA (see Table1), perhaps a holdover from the use of sodium acetate in conductivebuffers for RNA gels in the 1960's (7, 15). At that time, the NaAc wasadded with the intention to maintain the secondary structure of the RNA,most likely having no purpose when carried over to DNA electrophoresis(15). EDTA, introduced initially into the sample buffer to prevent RNAfrom remaining at the origin, is now superfluous, since most DNA samplesare readily soluble and since commonly used enzymes today would notcarry an undesirable enzymatic activity under electrophoretic conditions(15). The addition of free acid EDTA into the conductive media would beminimally conductive, for situations where EDTA may be specificallydesired. TABLE 1 Constituents and characteristics of conductive mediafor DNA electrophoresis. Voltage Tris Na+ Li+ range Media (mM) (mM) (mM)(V/cm)⁹ TAE¹ 40 6 0 5-10 TAE² 40 10 0 5-10 TBE³ 89 0 0 5-10 TBE⁴ 89 4 05-10 TBE⁵ 89 8 0 5-10 SCA⁶ 0 12.5 0 5-10 Na boric acid⁷ 0 10 0 5-50 Liboric acid⁷ 0 0 10 5-50 Li boric acid⁸ 0 0 1  5-150Protocols from:¹Maniatis (contains 2 mM diNaEDTA),²Hayward (2 mM diNaEDTA),³Invitrogen (2 mM free acid EDTA),⁴Maniatis (2 mM diNaEDTA),⁵USB (2 mM tetraNaEDTA),⁶novel media at 12.5 mM cation concentration.⁷novel media at 10 mM cation concentration and.⁸novel media at 1 mM cation concentration.⁹V/cm = voltage applied to electrophoretic rig, per cm of gel length toproduce optimal resolution of separated DNA fragments in 5 mm thickagarose horizontal gels.Li, lithium; Na, sodium.

These commonly used buffers thereby create a “runaway” positive feedbackloop of current and temperature (FIG. 2). For most TBBs, this positiveloop results in poor gel resolution at high voltage and a necessity forlow voltage runs (5-10V/cm).

Example 3—Alternative Media

We thereby explored alternative, simplified conductive media that couldmitigate this feedback loop. A reduced concentration of Tris-acetic acid(stripped of NaAc and EDTA) was sufficient for DNA electrophoresis (30mM Tris; adjusted to pH 8 with glacial acetic acid to about 20 mMacetate) (Table 1), while lower concentrations of this solution providedpoorer gel resolution (data not shown). This optimal Tris-acetic acidmedia (OTA) (Table 1) outperformed TAE and was comparable to TBE in thedesirable properties investigated (FIG. 1 a-c). OTA gels could be runfaster than TAE gels (i.e. at high voltage, 25V/cm) as well as atstandard electrophoretic conditions (10 V/cm) (data not shown).Interestingly, although chloride might not be the optimal anion forTBBs, a standard commercial TE solution at 3× provided adequate gelresolution (see Materials and Methods, data not shown).

Conductive media using low molarity alternative cations were explored.Media based on sodium chloride and NaAc (SCA) were derived empirically(FIG. 3 a-c). Combinations of particular concentrations (SCA islands)permitted high resolution of DNA fragments under standardelectrophoretic conditions (FIG. 3 b). Alternate anions could besubstituted into SCA; sodium phosphate, sodium bicarbonate, and sodiumsalicylate could replace sodium acetate in SCA (data not shown).Similarly, other cations, provided by potassium chloride with potassiumacetate or by ammonium acetate with ammonium chloride, could beadequately used at SCA concentrations (7.5 mM acetate and 5 mM chloride)(data not shown). FIGS. 4 b-d show the empirical nature of discoveringor “mapping” SCA. NaCl has a known ability to disrupt complexes of DNAwith itself or buffer, a property that may contribute to the observationof optimal composite media (11). Analysis of three distinct SCA mediaconcentrations (HiSCA, SCA, and LoSCA) showed all to have adequate gelresolution, with LoSCA conducting the lowest current and best resolutionover a prolonged time (FIGS. 4 b and c and data not shown). Therefore,LoSCA was chosen for further analysis of SCA gels. Although LOSCA mediaoutperformed other SCA points, we found that midSCA (see table 1 andFIG. 3 a) was less “finicky” as to tolerable ionic concentrations ascompared to LOSCA, which resided in a narrow area within the SCA islands(FIG. 3 a). Higher concentrations of sodium chloride produced a saltboundary which could presumably be avoided with reservoirs of largervolume (FIGS. 4 a and c).

We then explored the borate requirements of our sodium-based series oflow-conductant media Empirically, 10 mM sodium boric acid (10 mM sodiumprovided by 5 mM disodium borate decahydrate or by 10 mM sodiumhydroxide, adjusted with boric acid to a pH of 8) was excellent atstandard electrophoretic conditions (FIG. 4 a, see table 1 fordescription of media). Sodium boric acid (SB) resolved best within anarrow range of 7.5 mM and 12.5 mM (data not shown). Potassium boricacid (potassium hydroxide titrated to pH=8 with boric acid) wassimilarly excellent as a conductive medium (data not shown).

SB medium was able to essentially abrogate the “runaway” feedback loopof increasing current and temperature (FIG. 1 a-c). LOSCA performedbetter than TAE in analysis of the feedback loop (FIG. 1 a-c), yet wasunable to mitigate the feedback loop to the same extent as SB. SB hadonly slightly increased temperature and current over time and thusproved to be an outstanding conductive media for electrophoresis.

Extending our comparison of TBB and Tris-less media, it was of interestto directly compare Tris to sodium ions. Tris, spiked into SB, requirednearly ten-fold higher concentration to cause a comparably increasedcurrent in a Tris-less system, as compared to the amount of NaCl or NaAcrequired in a TBB system. This result was consistent with the highermolar conductivity of sodium ions (FIGS. 1 d,e) (16). Consequently, TBBmedia usually incorporate 40 to 80 mM Tris.

The new low-conductive media allowed achievement of ultra-fastelectrophoretic separation using higher voltages. For example, agarosegels using SB at high voltage (30V/cm or 300 volts in a small gel rig,see table 1) resulted in a high-resolution separation within 13 minutes(FIG. 4 b), similar to such a gel run at a standard voltage (10V/cm) for1 hour and 30 minutes (FIG. 4 a). Gel extraction of restriction-digestedplasmid DNA was performed in SB gels for cloning experiments (FIG. 4 c).A stock of 10×-50× can be stored without the occurrence of precipitationover time as occurs with tris boric acid. While SB is advantageous, aborate-free alternative is provided by SCA medium (see table 1) or bylithium acetate (table 1 and presented below).

The above study used agarose gels. SB was also successfully used innon-denaturing and denaturing (6%-20%) polyacrylamide gels. Denaturinggels with urea showed adequate electrophoretic resolution, optimallywith the inclusion of 1×SB and ficoll-400 in the formamide loadingsolution (data not shown). Non-denaturing gels (6% and 20%) were able toresolve 100 base pairs and below (data not shown). SB, in thepolyacrylamide system, reduced the current and implicitly the heatgeneration at high voltage compared to 1×TBE buffer. Polyacrylamidedenaturing and non-denaturing gels also performed adequately withpotassium boric acid (10 mM potassium ion) and SCA (data not shown).

Example 4—Electrolyte Exhaustion

SB (pH=8) had a delayed electrolyte exhaustion at constant voltage ascompared to other media tested (FIG. 5). Electrolyte exhaustion occurredat 3 hours for SB, but at less than one hour for TAE, as determined byobserving the current at a constant voltage (FIG. 5). In this regard, SBoutperformed every conductive media tested: SCA, LoSCA, TAE, and TBE.Indeed, TBE outperformed TAE, most likely due to the boric acid, whichby buffering the hydroxide production provides a continuing cathodicsource of borate for conducting current. Along similar lines ofexplanation, SB pH=9 exhausted more rapidly than SB at pH=8 (FIG. 5 a).At the lower pH, boric acid represents a larger reserve to replenishions at the cathode. One would expect that boric acid-containing mediacould be used for longer runs without recirculation. For prolonged runsinvolving a reuse of media, recirculation and replenishment of boricacid (H₃BO₃) and borate (borate acid ion, H₂BO₃—) from the anodicchamber to the cathodic is feasible, but acetate, once destroyed at theanode, cannot be recirculated. The substitution of sodium salicylate forNaAc in SCA solution illustrated this reaction class. The anodic chamberbecame bright yellow due to the oxidative decarboxylation of salicylatefollowed by oxidative meta-cleavage of the catechol intermediate to form2-hydroxy muconic semialdehyde (data not shown) (17). pH changes in theanodic and cathodic chambers of TBBs and sodium-based media were indeedobserved during electrophoresis (FIG. 5 c). In contrast to all othermedia tested, TBE and SB were able to maintain a constant pH of nearly 8in both electrode chambers (FIGS. 5 b and c). Of note, acetate mediashould not be considered as buffered solutions, when used at a pH rangedesirable for DNA.

Example 5—Miscellaneous Properties

We also demonstrated several interesting and expected properties that wenonetheless know to relate to some common misconceptions amonginvestigators that perform electrophoresis. First, an increased volumeof buffer in the gel rig increased both the current and the temperatureduring electrophoresis at constant voltage (data not shown). Someinvestigators regrettably presume that the addition of extra bufferwould act as a heat sink for the gel. Second, the voltage applied by thepower source greatly exceeded that applied to the gel. In all bufferedsystems tested, the measured voltage “seen” by the gel (using voltmeterprobes) was roughly half of the setting on the power supply when testedacross the gel (data not shown). Further, the potential differencesacross the “upper” and “lower” halves of the gel were equivalent andstable over the course of a standard electrophoretic run. Theelectrophoretic force experienced by each segment of the gel thus wasconsistent with the concept of field strength, calculated by dividingvolts by distance, although this would be modified by exhaustion ofindividual ionic species through migration (2,9). Most of the remainingvoltage drop and power consumption is assumed to be attributable to theelectrolysis of water. The values of field strength given in this reportconform to the convention in the literature to specify the voltagedelivered, rather than that experienced by the gel.

Third, in searching for a better conductive media as judged by reducedcurrent, temperature generation, and gel resolution, we found that TBEwas a better medium than TAE (FIGS. 1A-C, 5). Fourth, 5 mm thick gelswere adequate for horizontal electrophoresis, while thicker gelsproduced increased heating due to increased current (data not shown).Finally, DNA electrophoresis buffers are normally adjusted between pH7.9-8.0 but since nucleic acids are highly acidic, it is known that DNAelectrophoretic separation should withstand pH changes within a widerange (2). We found that most gels at various pH from 7.5 to 9.3produced similar results (data not shown). We also found thatlow-concentration conductive media did not “exhaust” faster, a favorablefinding that is attributable to a lower current which compensated forthe reduction in the ionic reserves.

In summary, it is possible to mitigate the “runaway” positive feedbackloop with new, simple conductive media, along with considerable savingsin cost and time (Table 1).

We roughly estimate that the new conductive media could save the UnitedStates over 90 million dollars annually, allowing better temperaturecontrol, improved portability and convenience by reduced power andamperage requirements of the power supply, and a decreased need for heatdissipation in the electrophoretic device.

It is instructive, in light of the above studies, to revisit the historyof the current buffers to examine how suboptimal buffers might have cometo dominate DNA electrophoretic technology in preference to simpler andbetter media. It is our thesis that the explanation lies in thesystematic development of these media which lacked a comprehensiveanalysis of the constituents. For example, borax and, later, variedborate solutions were found to allow the electrophoretic migration andthus separation of otherwise neutral carbohydrates, such as glucose andmaltose (20). Comparative studies found that, to drive the formation ofthe borate-carbohydrate complexes, one required an optimal pH as well ashigher concentrations of the borate solutions, such conditions allowingmaximal migration rates in an electric field. The later specification oftris as a favored counter-ion provided additional buffering ability andwould have mitigated the known and limiting problem of ohmic heating.

DNA, however, does not require full complexation with borate to provideoptimal electrokinetic behavior, for DNA is naturally charged in allsolutions in which it is chemically stable. Borate concentrations thusexceeded those needed for electrophoretic separation. Yet, there was nowa Catch-22 for any efforts to simplify the medium. The dilution ofborate in DNA electrophoretic separative media was limited by the poorresolution of low-conductance tris buffers, and the simple substitutionof a more electromotile counter-ion was limited by ohmic heating of thehigh-concentration borate solutions. Similar barriers impeded themodification of tris-acetate buffers. The substitution of a metal ion asthe predominant counter-ion required the simultaneous modification ofionic species and concentrations.

Example 6—Resolution of Small and Large DNA Fragments and of RNA

Materials and Methods. Gels were 1.0% agarose (Type I low EEO, Sigma,St. Louis, Mo.) unless otherwise indicated and contained 0.2microgram/ml ethidium bromide (Fisher Scientific, Fair Long, N.J.). Thepower source displayed current flow (milliamps) at set voltages (250,300, and 1000 volts (V)). ΔT (° C.) was calculated by subtracting theinitial from the final temperature of the media in the anodic chamber.All DNA electrophoretic runs used a horizontal rig (MGU-500, CBS, DelMar, Calif.) and had 650 ml total volume of medium in the reservoirs.Gels were 10 cm in length. 1 Kb-plus (Invitrogen, Carlsbad, Calif.) and20 bp (GenSura, San Diego, Calif.) DNA ladders were loaded as indicated.For DNA, loading media was an Orange G (Sigma) based 10% glycerol (USB,Cleveland, Ohio) in solutions to match the cognate 1× conductive mediain use.

Short oligomers of ssDNA were separated in 1 mM lithium boric acidmedium. A 35 bp oligomer was mixed in parallel with 36, 38, and 45 bpoligomers (40 ng each), respectively, and heated to 70° C. for 5 min todenature potential dimers. Samples were loaded at 370° C. and separatedfor 25 min at 29 V/cm.

For RNA gel electrophoresis, an RNA ladder (#361, New England Biolabs,Beverly, Mass.) was used. For each run, 200 ng of ladder in 1.8 uL ofloading medium (4.5% glycerol, 7.5% formaldehyde, 57% formamide, 40ug/mL ethidium bromide) was denatured at 70° C. for 2 min, placed on icefor 2 min and loaded onto denaturing gels containing 1% agarose, 0.67%formaldehyde, and either 5 mM sodium boric acid or 5 mM lithium acetatein the gel and reservoirs. Gels were run at 400 V (40 V/cm) for 10 minin a CBS scientific MGU-200T horizontal mini gel system. Current wasobserved by methods similar to those described for DNA electrophoresis.

Results/Discussion. Sodium boric acid (10 mM sodium) permittedhigh-voltage rapid DNA electrophoresis (18). Empirically, in specialtyapplications it proved possible to further reduce the ionicconcentrations and current of conductive media by another five- toten-fold. Salt solutions of alkali metals (lithium boric acid, rubidiumboric acid, potassium boric acid, cesium boric acid) and a simple,non-biologic buffer amine (ethanolamine with boric acid) were tested atvarious concentrations (19). At 1 mM cation concentration, DNA fragmentswere separated with minimal conductivity (FIG. 6A). Notably, thesesolutions separated small DNA fragments at a very high voltage (1000 V,100 V/cm, FIG. 6). These low-concentration solutions did not generatesignificant heat in an electrophoretic system, unlike commonelectrophoretic media, and thus were run roughly 15-fold faster than isconventional practice (FIG. 6A, TAE and TBE run at 5-10 V/cm; newconductive media, up to 150V/cm, not shown). Further, these low-molaritymedia served well in separating small DNA fragments in agarose gels thatnormally would require polyacrylamide (FIG. 6A and 6C). Electrolyteexhaustion was measured by observing the current over the course of theelectrophoretic runs; the current of the 1 mM solutions did not dropmore than 15% during these runs (FIGS. 6A and 6B).

Lithium boric acid outperformed other low molarity media in its lowconductivity and minimal heating (FIG. 6). One-mM lithium boric acid(3.0% agarose gel) was able to resolve 1-base pair differences betweenssDNA oligomers in the absence of a chemical denaturant and withoutrequiring high temperatures (FIG. 6C). Gel purification of an oligomerin 1 mM lithium boric acid yielded high recovery of the ssDNA fragment(Spin-X, Costar, Cambridge, Mass.)(not shown). Low molarity mediareadily permitted preparation of higher density agarose gels (3.0%agarose, FIG. 6C).

Although boric acid provides an exceptional anion for DNAelectrophoresis (1, 18, 19), we found that alternative non-borate anionsproduced greater separation of high molecular weight (>2.0 Kb) DNAfragments (not shown). Lithium acetate (5 mM)(1×) produced low currentand heat, thus allowing for fast separation of the longer DNA fragmentsin 1.0% agarose gels (FIG. 7A)(19). In comparison, TAE gels meltedwithin 30 min at such high voltage (30 V/cm, not shown).

Low-molarity media were also successful in separating RNA in agarose gelelectrophoresis (FIG. 7B). Sodium boric acid (5 mM, pH=6) (0.5×) andlithium acetate (5 mM) resolved RNA within 10 minutes (400 volts,40V/cm, FIG. 2C)(18). These low-molarity media resolved RNA under lowerheat and conductive conditions than the conventional MOPS medium (FIG.7B)(19).

A positive runaway feedback loop exists in DNA electrophoresis betweentemperature and current when using tris-based solutions (TAE and TBE)(FIG. 6A) (9, 18, 12). New conductive media mitigate this feedback loopand allow for ultra-fast separation of small and large DNA and RNAfragments in an easy-to-use agarose system (FIGS. 6 and 7). Lithium hadthe lowest current of the alkali metal series, consistent with itslarger shell of hydration. Conversely, and as expected, cesium andrubidium had the highest conductivity due to their smaller radii ofhydration (FIG. 6). One-mM solutions performed well in electrophoresisirrespective of concern for buffering capacity, and thus it is best tolabel these solutions as conductive media rather than as ‘buffers.’

For standard applications of slab gel DNA electrophoresis (100 bp to 5.0Kb separations), we recommend 110 mM sodium boric acid be used. Inspecial situations, such as high resolution separation of longer DNAfragments (>3.0 Kb) we recommend 5 mM lithium acetate (FIG. 7A). Whereadequate attention can be devoted to reduction of salt in the sampleanalyzed, 10 mM lithium boric acid is recommended for small andmid-sized DNA fragments (<3.0 Kb). 5 mM sodium boric acid and 5 mMlithium acetate media can be used in place of MOPS for RNA separation(FIG. 7B). One-mM lithium boric acid agarose gels can be used in placeof polyacrylamide for separation of small DNA and ssDNA fragments (FIG.6). Other choices are not precluded, but these appeared optimal underthe conditions tested.

Low-molarity media mitigates the positive feedback loop that exists withexisting media and can be used to separate very small or large fragmentsof DNA in agarose gels, outperforming the commonly used media in theabove-examined applications. These findings should improve the speed,cost-effectiveness, and practicality of many genetic-basedinvestigations.

REFERENCES

-   1. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989) Molecular    cloning: a laboratory manual (Cold Spring Harbor Laboratory, Cold    Spring Harbor, N.Y.).-   2. Aaij, C. & Borst, P. (1972) Biochim Biophys Acta 269, 192-200.-   3. Hayward, G. S. & Smith, M. G. (1972) J Mol Biol 63, 383-95.-   4. McDonell, M. W., Simon, M. N. & Studier, F. W. (1977) J Mol Biol    110, 119-46.-   5. Thorne, H. V. (1966) Virology 29, 234-9.-   6. Stellwagen, N. C., Bossi, A., Gelfi, C. & Righetti, P. G. (2000)    Anal Biochem 287, 167-75.-   7. McPhie, P., Hounsell, J. & Gratzer, W. B. (1966) Biochemistry 5,    988-93.-   8. Maniatis, T., Fritsch, E. F. & Sambrook, J. (1982) Molecular    cloning: a laboratory manual (Cold Spring Harbor Laboratory, Cold    Spring Harbor, N.Y.).-   9. Brody, J. R. and Kern, S. E. (2004) Analytical Biochemistry 333,    1-13-   10. Stellwagen, N., Gelfi, C. & Righetti, P. G. (2002)    Electrophoresis 23, 167-75.-   11. Stellwagen, E. & Stellwagen, N. C. (2002) Electrophoresis 23,    1935-41.-   12. Hjerten, S. (1973) Ann N Y Acad Sci 209, 5-7.-   13. Hawcroft, D. M. (1997) Electrophoresis (IRL Press at Oxford    University Press, Oxford N.Y.).-   14. Allen, R. C. & Budowle, B. (1994) Gel electrophoresis of    proteins and nucleic acids: selected techniques (W. de Gruyter,    Berlin; New York).-   15. Loening, U. E. (1967) Biochem J 102, 251-7.-   16. Ng, B. & Barry, P. H. (1995) J Neurosci Methods 56, 37-41.-   17. Dagley, S. (1960) Nature 188, 560-566.-   18. Brody, J. R. and Kern, S. E. (2004) Biotechniques 36, 214-216.-   19. Brody, J. R. and Kern, S. E. (2004) Biotechniques 37, 598-602.-   20. Foster, A. B. (1957) Adv Carbohydr Chem 12, 81-115.

1-335. (canceled)
 336. A gel for separating polynucleotides according tolength of the molecules comprising a matrix substance and a conductivemedium which comprises at least 0.5 mM anions in addition to anychloride anions which are optionally present, and less than 25 mM oftotal ions, wherein the conductive medium does not contain an organicamine biological buffer; and wherein said conductive medium comprisessodium as a cation and borate as an anion.
 337. The gel of claim 336,wherein the matrix substance is polyacrylamide.
 338. The gel of claim336, wherein the matrix substance is agarose.
 339. The gel of claim 336,wherein the conductive medium comprises a first and a second salt ofsodium; wherein the first salt is a chloride salt and the second salt isa borate salt, and wherein the conductive medium has a pH of between 6and 10, inclusive.
 340. The gel of claim 336, wherein the conductivemedium comprises less than 20 mM of total ions.
 341. The gel of claim336, wherein the conductive medium comprises at least 10 mM anions. 342.The gel of claim 336, wherein the conductive medium comprises at least0.5 mM sodium ion.
 343. The gel of claim 336, wherein the conductivemedium has a pH of 5.5 to
 10. 344. A solution for making a gel forseparating polynucleotides according to length of the moleculescomprising: a conductive medium which comprises at least 0.5 mM anionsin addition to any chloride anions which are optionally present, andless than 25 mM of total ions, wherein the conductive medium does notcontain an organic amine biological buffer; and a polymerizing agent forpolymerizing a gel matrix substance; and wherein said conductive mediumcomprises sodium as a cation and borate as an anion.
 345. The solutionfor making a gel of claim 344, wherein the conductive medium comprises afirst and a second salt of sodium wherein the first salt is a chloridesalt and the second salt is a borate salt, and wherein the conductivemedium has a pH of between 6 and 10, inclusive.
 346. The solution ofclaim 344, wherein the conductive medium comprises less than 20 mM oftotal ions.
 347. The solution for making a gel of claim 344, wherein theconductive medium comprises at least 5 mM anions.
 348. The solution ofclaim 344, wherein the conductive medium comprises at least 0.5 mMsodium ion.
 349. The solution of claim 344, wherein the conductivemedium has a pH of 5.5 to
 10. 350. An electrophoretic apparatus forseparating polynucleotide molecules comprising a gel, two or morereservoirs contiguous with the gel, and an anode and a cathode incontact with the reservoirs, wherein the reservoirs and the gel comprisea conductive medium which comprises at least 0.5 mM anions in additionto any chloride anions which are optionally present, and less than 25 mMof total ions, wherein the conductive medium does not contain an organicamine biological buffer; and wherein said conductive medium comprisessodium as a cation and borate as an anion.
 351. The electrophoreticapparatus of claim 350, wherein the conductive medium comprises a firstand a second salt of; wherein the first salt is a chloride salt and thesecond salt is a borate salt, and wherein the conductive medium has a pHof between 6 and 10, inclusive.
 352. The electrophoretic apparatus ofclaim 350, wherein the conductive medium comprises less than 20 mM oftotal ions.
 353. The electrophoretic apparatus of claim 350, wherein theconductive medium comprises at least 5 mM anions.
 354. Theelectrophoresis apparatus of claim 350, wherein the conductive mediumcomprises at least 0.5 mM sodium ion.
 355. The electrophoresis apparatusof claim 350, wherein the conductive medium has a pH of 5.5 to
 10. 356.A method of forming a gel for separating polynucleotides comprising:mixing a gel matrix substance and a conductive medium which comprises atleast 0.5 mM anions in addition to any chloride anions which areoptionally present, and less than 25 mM of total ions, wherein theconductive medium does not contain an organic amine biological buffer toform a pre-gel mixture; incubating the pre-gel mixture under conditionsin which a gel forms; and wherein said conductive medium comprisessodium as a cation and borate as an anion.
 357. The method of claim 356,wherein the gel matrix substance is polyacrylamide.
 358. The method ofclaim 357, wherein the pre-gel mixture comprises a catalyst or initiatorof polymerization.
 359. The method of claim 356, wherein the gel matrixsubstance is agarose.
 360. The method of claim 356, wherein theconductive medium is made by dissolving a solid mixture in water priorto the step of mixing.
 361. The method of claim 356, wherein theconductive medium is made by diluting a concentrated stock solution ofthe conductive medium in water prior to the step of mixing.
 362. Themethod of claim 356, wherein the conductive medium comprises a first anda second salt of sodium; wherein the first salt is a chloride salt andthe second salt is a borate salt, and wherein the conductive medium hasa pH of between 6 and 10, inclusive.
 363. The method of claim 362,wherein the conductive medium comprises less than 20 mM of total ions.364. The method of claim 356, wherein the conductive medium comprisesless than 20 mM of total ions.
 365. The method of claim 356, wherein theconductive medium has a pH of between 6 and 10, inclusive.
 366. Themethod of claim 365, wherein the conductive medium comprises less than15 mM total ions.
 367. The method of claim 356, wherein the conductivemedium comprises at least 0.5 mM sodium ion.
 368. A gel for separatingpolynucleotides according to length of the molecules comprising a matrixsubstance and a conductive medium which comprises at least 0.5 mM anionsin addition to any chloride anions which are optionally present, and oneto 25 mM of total ions, inclusive, wherein the conductive mediumcontains an organic amine biological buffer at a concentration of lessthan 10 mM; and wherein said conductive medium comprises sodium as acation and borate as an anion.
 369. The gel of claim 368, wherein thematrix substance is polyacrylamide.
 370. The gel of claim 368, whereinthe matrix substance is agarose.
 371. The gel of claim 368, wherein theconductive medium comprises a first and a second salt of sodium; whereinthe first salt is a chloride salt and the second salt is a borate salt,and wherein the conductive medium has a pH of between 6 and 10,inclusive.
 372. The gel of claim 368, wherein the conductive mediumcomprises less than 20 mM of total ions.
 373. The gel of claim 368,wherein the conductive medium comprises at least 0.5 mM sodium ion. 374.The gel of claim 368, wherein the conductive medium has a pH of 5.5 to10.
 375. A solution for making a gel for separating polynucleotidesaccording to length of the molecules comprising: a conductive mediumwhich comprises at least 0.5 mM anions in addition to any chlorideanions which are optionally present, and one to 25 mM of total ions,inclusive, wherein the conductive medium contains an organic aminebiological buffer at a concentration of less than 10 mM; and apolymerizing agent for polymerizing a gel matrix substance; and whereinsaid conductive medium comprises sodium as a cation and borate as ananion.
 376. The solution for making a gel of claim 375, wherein theconductive medium comprises a first and a second salt of sodium, whereinthe first salt is a chloride salt and the second salt is a borate salt,and wherein the conductive medium has a pH of between 6 and 10,inclusive.
 377. The solution of claim 375, wherein the conductive mediumcomprises less than 20 mM of total ions.
 378. The solution for making agel of claim 375, wherein the conductive medium comprises at least 5 mManions.
 379. The solution of claim 375, wherein the conductive mediumcomprises at least 0.5 mM sodium ion.
 380. The solution of claim 375,wherein the conductive medium has a pH of 5.5 to
 10. 381. Anelectrophoretic apparatus for separating polynucleotide moleculescomprising a gel, two or more reservoirs contiguous with the gel, and ananode and a cathode in contact with the reservoirs, wherein thereservoirs and the gel comprise a conductive medium which comprises atleast 0.5 mM anions in addition to any chloride anions which areoptionally present, and one to 25 mM of total ions, inclusive, whereinthe conductive medium contains an organic amine biological buffer at aconcentration of less than 10 mM; and wherein said conductive mediumcomprises sodium as a cation and borate as an anion.
 382. Theelectrophoretic apparatus of claim 350, wherein the conductive mediumcomprises a first and a second salt of; wherein the first salt is achloride salt and the second salt is a borate salt, and wherein theconductive medium has a pH of between 6 and 10, inclusive.
 383. Theelectrophoretic apparatus of claim 381, wherein the conductive mediumcomprises less than 20 mM of total ions.
 384. The electrophoreticapparatus of claim 381, wherein the conductive medium comprises at least5 mM anions.
 385. The electrophoresis apparatus of claim 381, whereinthe conductive medium comprises at least 0.5 mM sodium ion.
 386. Theelectrophoresis apparatus of claim 381, wherein the conductive mediumhas a pH of 5.5 to
 10. 387. A method of forming a gel for separatingpolynucleotides comprising: mixing a gel matrix substance and aconductive medium which comprises at least 0.5 mM anions in addition toany chloride anions which are optionally present, and one to 25 mM oftotal ions, inclusive, wherein the conductive medium contains an organicamine biological buffer at a concentration of less than 10 mM, to form apre-gel mixture; incubating the pre-gel mixture under conditions inwhich a gel forms; and wherein said conductive medium comprises sodiumas a cation and borate as an anion.
 388. The method of claim 387,wherein the gel matrix substance is polyacrylamide.
 389. The method ofclaim 388, wherein the pre-gel mixture comprises a catalyst or initiatorof polymerization.
 390. The method of claim 387, wherein the gel matrixsubstance is agarose.
 391. The method of claim 387, wherein theconductive medium is made by dissolving a solid mixture in water priorto the step of mixing.
 392. The method of claim 387, wherein theconductive medium is made by diluting a concentrated stock solution ofthe conductive medium in water prior to the step of mixing.
 393. Themethod of claim 387, wherein the conductive medium comprises a first anda second salt of sodium; wherein the first salt is a chloride salt andthe second salt is a borate salt, and wherein the conductive medium hasa pH of between 6 and 10, inclusive.
 394. The method of claim 393,wherein the conductive medium comprises less than 20 mM of total ions.395. The method of claim 387, wherein the conductive medium comprisesless than 20 mM of total ions.
 396. The method of claim 387, wherein theconductive medium has a pH of between 6 and 10, inclusive.
 397. Themethod of claim 396, wherein the conductive medium comprises less than15 mM total ions.
 398. The method of claim 387, wherein the conductivemedium comprises at least 0.5 mM sodium ion.